


The Time Lord Engine

by Ladyhazle



Category: Doctor Who, Doctor Who (2005)
Genre: Betrayal, Clara Oswald - Freeform, Deception, F/M, Gen, Handcuffs, Love, Post Episode: s04e08-09 Silence in the Library/Forest of the Dead, Reunion, Run, The Doctor Dances, Twelfth Doctor Era, slight of hand
Language: English
Status: In-Progress
Published: 2014-12-29
Updated: 2015-10-19
Packaged: 2018-03-04 04:01:10
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 4
Words: 4,670
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2908589
Author URL: https://archiveofourown.org/users/Ladyhazle/pseuds/Ladyhazle
Summary: <blockquote class="userstuff">
              <p>Someone has resurrected Professor River Song and the consequences may cause the destruction of the universe itself!</p>
            </blockquote>





	1. Science and Religion

**Author's Note:**

> Disclaimer: This is fan fiction. I do not lay claim to anything Doctor Who, except my *fantasies. You can't have those. :-)
> 
> *Obviously, I am a Doctor\River Song shipper who would love to see Capaldi's Doctor with River. I like to write stories that are post The Library\Forest of the Dead because that means that River is truly alive again and not just a data ghost, or a younger version of herself.

     The Doctor lay on his left side, sprawled upon the expanded metal catwalk that surrounded the brightly illuminated console of his oft times trusty Type-40. He had a rather nasty gash above his right eye. The blood was just now drying where it had run down the side of his face. The little bit that made it into his hair line, contrasted sharply with the short, soft gray hair there.

     His black coat and trousers had seen better days. They were dirty, and jagged threads protruded from several slices where the material of his coat caught on something sharp, splitting it wide open to reveal the bright red satin liner inside.

     The abused Time Lord groaned deeply within his chest. He slowly rolled over onto his back and looked up at the console. He immediately regretted the motion. His long fingers went to his throbbing head, finding the bloody wound in the process. The Doctor opened his eyes just a bit to look at the crimson gore smeared on his fingertips. It took a moment for his usually intense greenish eyes to adjust to the brightness around him. The Doctor's vision was blurry. He imagined that it was likely from the blow to his thick skull.

    

      “Well now, somebody obviously didn't like you having a closer look around, did they?”

    

     The Doctor's hearts skipped at the sound of the low, sultry female voice that penetrated the quiet. He fought back the pain in his head to try to look around. His ears caught the sharp, 'click' 'click' 'click' of high heels striking the metal ramp just inside the TARDIS doors. The Doctor's restricted optics managed to spy two sparkling silver high heeled shoes making their way toward him. He followed the shiny material up to the ruffled hem of a black cocktail dress. A flash of creamy skin revealed the slit in the angled line of the skirt that went up to the mid thigh of its bearer. An amble bosom pressed against the sweetheart neckline of the strapless gown. When the ancient man of time's eyes came up to view her hair, his hearts nearly stopped.

    

     “River,” he breathed, rolling the 'R's' delightfully.

    

     “Hello Sweetie,” River greeted him as usual. “Yes, I'm really here, my love.” River leaned down and offered her hand. The Doctor waved off the help and gathered his feet under himself. He pushed himself up to stand and staggered a little. River grabbed onto him, putting her hands on both of his arms, until he had his balance again.

     As casually as he could, the Doctor stepped back from her hands and leaned against the control panel for support. River immediately understood that this regeneration did not feel nearly as comfortable with a hands on approach as his previous incarnation had. She came to stand next to him instead, giving the Time Lord just enough of the space he required.

    

     “How,” he asked. His fierce eyebrows were frowning low over his eyes in pain.

     River shrugged, a bit too casually. “Oh, you know me, dear. I'm not one to stay in a cage for very long.” She removed a roll of lipstick from somewhere on her person, and re-applied the color to the already vibrant shade of red gracing her beautiful, full lips. “Not even one resembling a bookshelf,” she added. The Doctor's only reaction to her latter comment, was to grip the edge of the console so hard with his right hand, that his knuckles turned a harsh white.

    

      “I don't understand,” the Doctor said. He was having a hard time thinking. His head hurt so damn bad!

    

     “Shocker,” River joked without much humor in her voice.

 

     “River,” the Doctor warned, his voice a low growl.

 

     “Someone wanted me out of the Library, more than you did, Sweetie. It's really that simple.”

 

     “That,” the Doctor whispered with his eyes shut, “is not possible.”

 

     The Doctor rubbed his temple just below the bloody gash. The motion drew attention to the wound and made River soften a bit. She moved around the console to a hatch marked with a large red cross. River opened the lid to reveal a fully stocked first aid kit built right into the control panel.

 

     “Where the devil did that come from,” he asked. His vision was finally returning to normal. The banging away in his head had not, however. It was making it very difficult for him to form complete thoughts, let alone full sentences.

 

     “You were unconscious for awhile. I got bored. I thought it would help,” River explained while she prepared the necessary supplies to clean and bandage the wound marring the Doctor's already roughhewn features. The Doctor flinched hard when she tried to touch the sterile wipe to the dried blood on his face. She wasn't sure if it was because of the pain, or because he didn't want her to touch him. Either way, River was annoyed.

 

     “Stand still, you stubborn idiot,” she grouched, “I'm trying to help you.”

 

     Instead of standing still as instructed, the Doctor suddenly grabbed River's wrist. He scowled deeply at her, moving in close so that there were only a few inches between their faces.

 

     “How, exactly, did you get out,” he demanded quietly. His underlying Scottish growl seemed to deepen as he grew angry. “Who did it?” He was not really asking. The Doctor expected an answer. River knew that, which was exactly why she didn't give him one right away.

 

     “Speaking of books,” she said, suddenly changing the subject. River spun away from the Doctor, her skirt fluttering as air caught beneath it. She touching the console controls reverently here and there as she went, “I wanted to thank you for leaving my journal, and my sonic behind.”

 

     The Doctor turned to glare at her across the controls.

 

     “Those were shielded.”

 

     River nodded. “Yes, I know. Hidden in plain sight. Brilliant,” she exclaimed.

 

     “Compromising the shield would have set off alarms in the TARDIS,” he said. “I would have known. I... I would have gone back.”

 

     River smiled a genuine smile. “You rarely stop moving, Doctor. You could have easily been running for your life, and missed them.”

 

     He realized that she was giving him an out, and that he had better take it if he ever wanted to get back around to the question she was avoiding. The Doctor nodded and closed his eyes. He lifted his hand to rub at his temple again. This time, the gesture was one of frustration, instead of self soothing. He shook his head and ran his hand through his hair.

 

     “You're right,” he said, giving her a small, tired smile, “I was probably out saving the children of Earth, again. They seem to require it so often.”

 

     “Yes, they do.”

 

    “Are we going to continue to banter, here, all the while,” the Doctor asked, “or are you going to answer my question?”

 

     River casually made her way back around the console to stand near the Doctor. She longed to take his hand, or perhaps feel the graying curls of his hair between her fingers, if only for a moment. Being so close to him, and yet so far away was agonizing. As much as she longed to, River did not close the gap between them.

     The Doctor could tell that River was restraining herself. He knew she wanted to reach out to him. If he was going to welcome the touch of anyone, besides holding hands with Clara, it would be from River Song. He wasn't ready. Not yet. The Doctor still wasn't completely convinced that any of it was real. He needed more answers.

 

     “The Vaticoracle are quite skilled with trace DNA,” she said simply.

 

     The Doctor raised an eyebrow.

 

     “Since when,” he asked skeptically.

 

     River shrugged her bare shoulders. “A few centuries. So I'm to understand.”

 

     “The Vaticoracle are a religious order.”

 

     “Apparently,” River answered, “a few hundred years ago, they found science as well.”

 

     “Science and religion,” he said, “seems a bit contradictory.”

 

     “Not to them,” River pointed out, “and I, for one, am grateful.”

 

     “Despite what you may believe, River,” he explained, “I too am grateful. What I want to know, however, is did those religious scientist also find violence? The Vaticoracle that I know of, are not nearly as heavy handed as the ones that I met earlier.”

 

     River smiled. “You can be rather rough in your verbal encounters, my love,” she said.

 

     The Doctor surprised her by quickly closing the space between them and taking her face in his hands. His flesh was warm on hers. Her hearts raced and her skin flushed with the intimate touch. She had to remember to breath. River looked into his intense eyes and tried so very hard to keep tears from filling her own.

 

     “Who guided them to you, River,” he asked in a deep, hushed tone. “I know they don't just go wanderin' about the galaxy, looking for trace DNA. Who instructed the Vaticoracle to resurrect _you_?”

 

     When River closed her eyes, a tear did slip free. It made a line down her face that ended when it met with the flesh of the Doctor's long thumb.

 

     “My Mistress,” River whispered.

 

 


	2. The Doctor and The Puppet

**Summary for the Chapter:**

> The Doctor dances into River's embrace and goes willingly into Missy's trap.

     "You're not serious," the Doctor said and dropped his hands away from River's face. She immediately missed the feel of his warm skin on hers.

 

     “You didn't really believe that she was dead, did you?”  
 

     The Doctor ran his hand over his face and turned away from River.

 

     “For the universes sake, I think I hoped so,” he replied quietly.

     The Doctor spun back around suddenly. His mind was clearing, as his advanced Time Lord genetics were repairing his wound at an accelerated rate. He waved his fingers in her direction, rolling his wrist for emphasis.

 

     “So, what, are you so angry with me for abandoning you, that you've become her puppet now,” he asked rudely.  
 

     River's hand swung out so fast, that the Doctor didn't even have a chance to flinch before the flesh of her palm met with his cheek. The force of the blow threw his head to the side and he staggered again, barely staying on his feet. River knew that if he was being blunt, he must be feeling better, so she had no immediate regrets about striking him so soon after his rough handling by the Vaticoracle.

     It took the Doctor a full moment to recover. He turned slowly back to River and looked into her eyes. She did not back down from his soul searching gaze.  
 

     “Try again, Sweetie,” she asked with an eyebrow raised over her piercing glare.

 

     “Why are you here, River?”  
 

     “She wants you,” River explained in a soft, slightly wounded tone, “and I'm the lure.”  
 

     “So, a puppet after all?”  
 

     For the flash of a second, River looked as though she wanted to smack him again. The tension suddenly melted off of her body and she slumped back against the TARDIS controls. Seeing the fight go out of River Song made the Doctor's hearts clench. This time around, he could certainly be a bit on the callous side, but he was not a monster.

     He made a show of walking around the console, fiddling with the controls and pretending to study the computer screen. The Doctor spoke without looking at his wife.  
 

     “How am I to spring the trap, then,” he asked. His gravely voice was husky with an attempt to smother his emotion. Their chins came up at the same time and they looked at one another across the console.  
 

     “I am sorry, my love,” River whispered sincerely.  
 

     “Never mind that now, dear, just answer my question,” the Doctor replied.  
 

     “Have you still got a bow-tie,” she asked with a coy smile spreading across her full red lips. The Doctor raised a questioning eyebrow. River shrugged.  
 

     “There's a party going on out there, Doctor, and I need you to dance with me,” River explained.  
 

⓬⓬⓬⓬⓬⓬⓬⓬⓬⓬⓬⓬  
 

      The Doctor stepped out of his TARDIS with River Song on his arm. At her behest, he had changed into a stylish midnight blue, modern cut tuxedo, with matching trousers. His bow-tie was black, to match the shiny Loake loafers that he refused to take off. The striking couple drew quite a lot of attention.  
 

      The Doctor was surprised to find that while he was unconscious, the room he landed in had been transformed. It was, in fact, a ballroom that was now filled to the brim with well dressed guests of all shapes, sizes, colors and affiliations. The universe was fairly well represented, as far as the Doctor could tell. The Time Lord took careful note of the Vaticoracle priests standing on the perimeter of the ballroom.

      Guarding against what, exactly, he wondered.  
 

      River's laughter filled the ballroom as the Doctor suddenly twirled the Professor onto the dance floor without warning. For a few precious seconds, it was almost like old times. No pretending, just an old married couple, enjoying their treasured time together. Minus the fumbling and ridiculous dance moves, of course. This version of himself was refined, precise in his movements and exuding confidence. Within those fleeting moments, the Doctor was able to forget his aversion to the touchy feely stuff.  
 

      After a few more spins, the Doctor let his eyes casually peruse the ballroom. He counted twenty Vaticoracle priests. No one else seemed out of place at the party. He did not spy Missy lurking anywhere. River had only been able to tell him what she was expected to do to lure him into the trap. Missy had not conveyed the entire plan to her puppet. She would want to spin those details to the Doctor in person. His only real concern was finding a way to release River from her “contract” with the Mistress and then stop the madwoman's plans, whatever they were, from coming to fruition. It was always easier said than done, he knew.  
 

      “Shall we get on with it,” he asked, pulling River closer so that he could speak without others hearing.  
 

      “Are you so eager to be rid of me, Doctor,” River asked. Her breath tickled the tiny hairs on the Time Lord's cheek.  
 

      “No, but I need answers that only Missy can give me,” he replied.  
 

      “She's going to use us against each other, you know that? Can you still be hurt by me, my love,” she asked. Her insecurity was plain as day. The Doctor's answer was simple:  
 

      “Yes.”  
 

      River forced the tears to stay where they belonged. She smiled a shining smile at her husband and took a deep, steadying breath.  
 

      “Ready,” she asked. The Doctor nodded once.  
 

      “I'll make it a good one,” River said nostalgically.  
 

     “You bloody well better,” the Doctor said in a reversal of a their roles so long ago in a different time and place.  
 

     They leaned in together and captured each others lips in a long-awaited, passionate kiss. River's left hand clenched his shoulder. Her other hand ran through his silver curls. His tongue pressed against her swollen red lips. River's fingers curled against his scalp, sending a tingling sensation down the length of his lean frame. Warmth spread through the Doctor's body as River parted her lips. The Doctor's own hand clench into a fist, balling the fabric of her slinky dress at the base of her spine. The heat was damn near overwhelming. He was fully aware of how incredibly sexy River Song was, but the roused Time Lord was also fairly certain that it was her hallucinogenic lipstick causing the heat to rise, instead.

     It was over far too soon for the Doctor. River's old standby performed its trick neatly, and when he opened his eyes, River was nowhere to be found. The Doctor was alone in the middle of the ballroom. The guests had disappeared and he was surrounded by his worse nightmare.

     Twenty Daleks around the perimeter of the room, screamed his name. Their maniacal voices grew louder with each chant and exclamation of 'Exterminate!'

    

     The Doctor searched quickly for an escape.  
 

      “Doctor!”

      He spun on his heels to find Clara near an exit. She was holding her hand out to him. Her big round eyes registered fear and the need for expediency.  
 

     “This way, Doctor,” she yelled across the space to him. “Run!”  
 

     He did not hesitate to close the distance between he and his companion. The Doctor took Clara's hand and they ran for their lives.


	3. The Puppet's Ruse

**Notes for the Chapter:**

> I really do apologize for the time it has taken me to update, and also for the length of this chapter. More to come, and quicker if I can possibly help it! Thank you for your readership.

### THREE:

#### The Puppet's Ruse

 

"You're not, Clara Oswald," the Doctor said abruptly and slid to a stop in the middle of the long, barren hallway, just outside of the Dalek filled ballroom. Clara's hand was jerked out of his when he stopped. She turned back to him, frantic.

"Of course, I'm Clara. Doctor, please hurry."

The Doctor's long fingers wiggled at the end of his waving hand as he tried to remember something very important. Clara came back to him and grabbed onto the sleeve of his midnight blue tuxedo jacket.

"We're running out of time," she warned him with a quick glance around his shoulder.

"You are not Clara," the Doctor insisted with an intense stare aimed down at his companion, "And those, those are not Daleks back there. I know that. The effects of hallucinogens are weakened on me. I could recall, if I wanted to."

"But, you're not supposed to do that, remember," Clara asked.

The Doctor looked down at Clara hard. The worry on her face melted and she smiled up at him.

"Do you trust me, Doctor?"

"I do," he answered.

"Then do as you're told, and follow me," Clara said, taking up his hand again. The Doctor allowed the young woman to lead him down the hallway at a brisk pace. They turned right when the choice presented itself. Clara stopped in front of a large steel door. There was a tiny window three quarters of the way up the door. It looked suspiciously like the entryway to a prison cell.

Clara knocked. The sound echoed down the hall. The Doctor's attention was drawn back the way they had come, by the vibrations of Clara's rapping knuckles. He felt like he was moving at half-speed. The Doctor blinked. The hallway was now filled with Vaticoracle priests, marching in sync toward the Time Lord and his companion. The priest's burgundy robes swished around their feet, making the Doctor think of a river of blood rushing down the corridor, eager to drown him.

His hearts hammered in his chest and sweat broke out on his pale forehead. He turned to Clara, to warn her, but his impossible girl was no longer there. The steel door stood open, revealing a lone metal chair, sitting in the middle of the barren room. A single light hung from the high, just out-of-view ceiling, creating a pool of illumination around the intimidating piece of furniture.

The Doctor barely had time to form his next thought before the red river caught up to him. The priests swarmed around the Doctor, pushing him into the room and guiding him to the chair. They did not speak. The sounds of their robes whispering against the smooth floor, and the shuffling of their efforts to move the Doctor along, were the only sounds in the room.

He was so focused on remembering the thing he wasn't supposed to be remembering, that he barely felt the his arms being pulled behind him and the cold metal handcuffs locked into place around his boney wrists.

It wasn't until her voice echoed out of the shadows that the Doctor's reality exploded back into sharp and horrifying focus.

“My, my, my,” Missy exclaimed with a flourish of her hand as she entered the light pooling around the Doctor's chair, “Getting yourself caught just so that you could hear my devious plans in person... I'm flattered, Doctor,” she said. 

“Don't be flattered, be afraid,” Missy answered herself, mimicking the Doctor's deep brogue. Her hysterical laughter sent chills down the Doctor's spine. A change in gender had done nothing to calm the level of insanity his childhood friend possessed.

“Have you finally stopped being surprised to see me pop up over and over again, dear?”

“What have you done to River,” the Doctor asked pointedly, ignoring Missy's pout.

She sighed shortly, a little disappointed in cutting to the chase, and then her face spread into a wicked grin. “And there it is, your Achilles' heel. Love,” Missy said, sauntering closer to the Doctor. “Will you never learn how easily it can be used to hurt you?”

“Will you never learn that it's worth every bit of pain,” he asked his nemesis quietly in return.

A twitch of Missy's right eye was the only sign of change in the otherwise unflappable psychopath. She reached out and grabbed his chin between her index finger and her thumb. He glared up at her.

“I'm going to cause you a lot of pain, Doctor,” she promised and placed a quick kiss upon the tip of his nose. She stood back up.

“Melody, dear,” she called out to the shadows. River stepped into the light. “Would you please bring the Doctor's TARDIS around for me?”

“Yes, Mistress,” River replied in a flat, lifeless tone. The Doctor's hearts clenched with sorrow for River as he watched her leave. Seeing her so subdued was hell. He couldn't even tell if she was faking it, or not. Where was the sultry, sassy woman who had picked him up off of the TARDIS floor, talked him into dressing up and then twirled around a dance floor with him, just a little while ago, he wondered.

“Oh, just a little control mechanism I had the Vaticoracle put into her DNA when they re-stacked it,” Missy said suddenly, as if she had heard his thoughts. He raised an eyebrow at her. She was smiling down at him with such pleasure. He wanted to be sick.

The TARDIS materialized at the edge of the pool of light with all of the familiar grinding and wheezing noises the Doctor so loved to hear. River exited the time machine and handed Missy the key.

“Did he not teach you how to perform a textbook landing, child,” Missy asked, putting her fingers to her head as if the sound had caused her a headache.

River turned her eyes down to the floor. “My apologies, Mistress. I suppose I left the brakes on,” River said. Missy threw up her hands and spun on her heels.

“Of course you did! Don't do it again, I despise that racket.”

River lifted her chin and looked directly into the Doctor's eyes while Missy's back was turned. His pulses raced.

Good girl, he thought without letting any of the emotion cross his face.


	4. World Building

**Summary for the Chapter:**

> Missy terrifying plan is unfolding.

**Notes for the Chapter:**

> This is a VERY short chapter. I am re-evaluating this story based on what we know of Missy in the current season.

* * *

The Doctor's skin crawled. The goose flesh radiated away from where Missy's breath disturbed the tiny hairs on the lobe of his left ear. It wasn't the tickle that made his skin crawl. It was the words that she had just whispered there.

  
  


_New Gallifrey._

  
  


The notion of it was both exciting and terrifying.

  
  


The sparkle in her eyes as she pulled back, just enough for him to see her face, did nothing to alleviate the knot that was forming in the Doctor's guts. She was overjoyed. She was sure she could do it. The Doctor was suddenly very sure he did not want to know _how_ she was going to accomplish it.

The look on his face must have given him away. Missy's lips curled up in the corners as she smiled wickedly, inches from his face. She gripped his shoulder. Her polished nails dug into the fabric of his tuxedo jacket.

  
  


“I have a very important part for you to play in this brave new world, my friend.”

  
  


“Not interested,” the Doctor replied.

  
  


“Oh,” Missy pouted, “but it's so exciting! I'm going to be using technology that hasn't been seen in several millenia.”

  
  


“You're going to re-build the Looms,” the Doctor guessed.

  
  


Missy stepped back so that she could clap for him and his very good guess.

  
  


“What do you need me for, then,” he asked.

  
  


“Oh, not just you, dear. I'm going to need your TARDIS, and her child as well.”

  
  


“What for,” the Doctor asked, his lack of patience showing.

  
  


“Regeneration energy, of course,” Missy answered.

  
  


The Doctor felt an edge of relief knife through his growing despair. He found and held River's eyes. She was working hard to keep them very empty. He always knew better. He caught a brief flash of warning cross her blue depths, but his mouth was already open, words slipping passed his thin lips.

  
  


“River doesn't have any regeneration energy left,” he ignorantly informed Missy. The sly, knowing smile that melted across her face was vicious.

  
  


“I don't regret to inform you, Doctor, that the Sisterhood of Karn now have competition. Your beloved has been completely restored to her original self,” Missy explained. “She is no longer the fool that ignorantly gave away her gift to some bumbling idiot with a screwdriver, and a box.”

A large part of the Doctor was overjoyed for River. She deserved it far more than he ever would. Of course, now she could also be used for Missy's evil plan, and that scared the hell out of him.

  
  


The Doctor looked again at his wife. Yes, now he could see it. A sparkle in the eyes. He should have noticed it before, really. 

I dare not start being a close-minded old fool now. he thought. Not after getting along for nearly two and a half thousand years being an open-minded one. 

  
  


"My congratulations to the Vaticoracle priests, slash, scientist," he said as calmly as he could. "With that kind of ability, you just have to wait a few hundred years and you'll have Time Lords and Ladies running all about. No need for me, or River in your silly, world-building plans."

  
  


"Well," Missy drawled out, "where's the fun in that? Besides, you know me, Doctor, I get bored. I have a very short attention span."

  
  


"Yep. An understatement," the Doctor replied while ever-so-slightly glancing passed Missy, to see River cross her arms over her chest and pretend to be bored. It was time.

  
  


“Okay, speaking of bored,” The Doctor said with a raise of one sharp eyebrow, “I've heard your bad plan and it's time to get up, out of this very hard chair, take my wife, and my box, and fly away to someplace, much more interesting.”

  
  


“And just how do you expect to do that,” Missy asked, folding her hands in front of her and looking down at the Doctor with mock pity.

“Well, you know,” he replied, “A lot of good came from me knockin' about with Professor River Song, all those years.” He smiled at River. She smiled back. “You get to hone some skills. One, in particular, I used quite a lot. Sometimes out of necessity... And sometime just for fun.” He winked at River and she grinned brilliantly. She knew.

  
  


“What in the name of the Gods are you droning on about now, Doctor,” Missy asked.

  
  


The TARDIS suddenly started grinding away, signaling her exit from the room. Missy spun on her heels in surprise. The Doctor jumped out of the chair, free of the handcuffs and latched them around Missy's wrists as quickly as he could.

  
  


“Handcuffs. Nice little trinkets. Rough on the skin though,” he whispered in her ear.

  
  


“Doctor,” River shouted as she tossed something to him. The Doctor caught River's sonic screwdriver and aimed it at the handcuffs that now encircled Missy's feminine wrists. They weren't going to hold her any more than they had the Doctor, but with some help from the sonic, it might buy them some time for their escape.

  
  


The Doctor pocketed the sonic out of habit and grabbed River's hand as they made for the big metal door. They were passing through into the hallway when the room behind them echoed with Missy's frustrated scream.

 

 


End file.
